One of the flaws in Ann Coulter's arguments in Godless is the fact that she believes that mutations arise already labeled neutral, beneficial, or non-beneficial, as if God had willed it so. Mutations do not arise in a vacuum, however, and any mutation is potentially any of these. When one says that a mutation (or adaptation) is beneficial, this must be taken in context with the vehicle's (organism's) genetic structure, environment, the existence of predators and competitors, the potential costs of this benefit as opposed to other benefits that could have evolved instead, etc. That a mutation carries an advantage in its particular context does not mean that the resulting adaptation is perfect, or that "things came together in perfect harmony" (as I often hear people say), or that the adaptation would even be considered adequate given fewer external constraints!
"It is simply meaningless to speak of an absolute, context-free, phenotypic effect of a given gene."--Dawkins
6 Constraints on "Perfection," or 6 Objections to Naive Adaptationism
-Time lags--the animal observed is "out of date," built under the influence of genes selected in an earlier era under different conditions. (The "lag load")
-Historic constraints--natural selection, having no foresight, modifies existing structures for new uses, leading in many cases to an obviously suboptimal formation, which nevertheless carries an advantage over no such formation at all.
Two species can respond to the "same selective forces in slightly different ways." --Lewontin
-Available genetic variation--"No matter how strong a potential selection pressure may be, no evolution will result unless there is genetic variation for it to work on."
-Constraints of Costs and Materials--adaptive organization is a "tangle of compromises."-Imperfections at one level due to selection at another--again, natural selection has no foresight.
-Mistakes due to environmental unpredictability or "malevolence"--adaptation to conditions is statistical in terms of success; moment-by-moment changes in an environment can trip up even the most successful animal. Moreover, manipulation of one animal by another can exploit the victims abilities, which in this context become disadvantages. The "loser" of this arms race may develop the ability to resist such manipulation; may find the manipulation beneficial to itself as well or may shape it to be such; or may actually go extinct, which does not necessarily benefit the aggressor.